data_1F7N # _model_server_result.job_id '_lofPhY7wIiX_IuZUwJBCQ' _model_server_result.datetime_utc '2024-12-26 12:05:10' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 1f7n # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":337}' # _entry.id 1F7N # _exptl.entry_id 1F7N _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 1F7N _cell.length_a 79.13 _cell.length_b 79.13 _cell.length_c 87.21 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1F7N _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA,PQS trimeric 3 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PQS trimeric 3 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,H 1 1,2,3 B,F,G,I 2 1 B,F,G,I 3 1,4,5 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 4 'crystal symmetry operation' 2_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 39.565 68.52859 0 5 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -39.565 68.52859 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 G N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A OD1 ASP 64 A ASP 64 1_555 C MG MG . A MG 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc2 A OD1 ASP 64 A ASP 64 2_555 C MG MG . A MG 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc3 A OD1 ASP 64 A ASP 64 3_555 C MG MG . A MG 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc4 C MG MG . A MG 137 1_555 H O HOH . A HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.953 ? metalc ? metalc5 C MG MG . A MG 137 1_555 H O HOH . A HOH 404 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.953 ? metalc ? metalc6 C MG MG . A MG 137 1_555 H O HOH . A HOH 404 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.953 ? metalc ? metalc7 D MG MG . A MG 138 1_555 H O HOH . A HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.045 ? metalc ? metalc8 D MG MG . A MG 138 1_555 H O HOH . A HOH 404 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.045 ? metalc ? metalc9 D MG MG . A MG 138 1_555 H O HOH . A HOH 404 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.045 ? metalc ? metalc10 D MG MG . A MG 138 1_555 H O HOH . A HOH 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.844 ? metalc ? metalc11 D MG MG . A MG 138 1_555 H O HOH . A HOH 412 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.844 ? metalc ? metalc12 D MG MG . A MG 138 1_555 H O HOH . A HOH 412 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.844 ? metalc ? metalc13 F MG MG . B MG 120 1_555 B OD1 ASP 64 B ASP 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.002 ? metalc ? metalc14 F MG MG . B MG 120 1_555 B OD1 ASP 64 B ASP 264 3_565 ? ? ? ? ? ? ? ? ? ? ? ? 2.893 ? metalc ? metalc15 F MG MG . B MG 120 1_555 B OD1 ASP 64 B ASP 264 2_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.942 ? # _chem_comp.formula 'C9 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id UMP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DUMP # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag N1 C2 UMP sing 358 n n N1 C6 UMP sing 359 n n N1 C1' UMP sing 360 n n C2 N3 UMP sing 361 n n C2 O2 UMP doub 362 n n N3 C4 UMP sing 363 n n N3 HN3 UMP sing 364 n n C4 C5 UMP sing 365 n n C4 O4 UMP doub 366 n n C5 C6 UMP doub 367 n n C5 H5 UMP sing 368 n n C6 H6 UMP sing 369 n n C1' C2' UMP sing 370 n n C1' O4' UMP sing 371 n n C1' H1' UMP sing 372 n n C2' C3' UMP sing 373 n n C2' H2' UMP sing 374 n n C2' "H2''" UMP sing 375 n n C3' C4' UMP sing 376 n n C3' O3' UMP sing 377 n n C3' H3' UMP sing 378 n n C4' O4' UMP sing 379 n n C4' C5' UMP sing 380 n n C4' H4' UMP sing 381 n n O3' HO3' UMP sing 382 n n C5' O5' UMP sing 383 n n C5' H5' UMP sing 384 n n C5' "H5''" UMP sing 385 n n O5' P UMP sing 386 n n P OP1 UMP doub 387 n n P OP2 UMP sing 388 n n P OP3 UMP sing 389 n n OP2 HOP2 UMP sing 390 n n OP3 HOP3 UMP sing 391 n n # _atom_sites.entry_id 1F7N _atom_sites.fract_transf_matrix[1][1] 0.012637 _atom_sites.fract_transf_matrix[1][2] 0.007296 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014592 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.011467 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 MG A 1 137 1 MG MG . D 2 MG A 1 138 3 MG MG . E 3 UMP A 1 139 118 UMP UMP . F 2 MG B 1 120 2 MG MG . G 3 UMP B 1 337 318 UMP UMP . H 4 HOH A 1 401 401 HOH H2O . H 4 HOH A 2 402 402 HOH H2O . H 4 HOH A 3 403 403 HOH H2O . H 4 HOH A 4 404 404 HOH H2O . H 4 HOH A 5 405 405 HOH H2O . H 4 HOH A 6 406 406 HOH H2O . H 4 HOH A 7 407 407 HOH H2O . H 4 HOH A 8 408 408 HOH H2O . H 4 HOH A 9 409 409 HOH H2O . H 4 HOH A 10 410 410 HOH H2O . H 4 HOH A 11 411 411 HOH H2O . H 4 HOH A 12 412 412 HOH H2O . H 4 HOH A 13 413 413 HOH H2O . H 4 HOH A 14 414 417 HOH H2O . H 4 HOH A 15 415 418 HOH H2O . H 4 HOH A 16 416 419 HOH H2O . H 4 HOH A 17 417 420 HOH H2O . H 4 HOH A 18 418 421 HOH H2O . H 4 HOH A 19 419 423 HOH H2O . H 4 HOH A 20 420 424 HOH H2O . H 4 HOH A 21 421 425 HOH H2O . H 4 HOH A 22 422 427 HOH H2O . H 4 HOH A 23 423 428 HOH H2O . H 4 HOH A 24 424 429 HOH H2O . H 4 HOH A 25 425 430 HOH H2O . H 4 HOH A 26 426 431 HOH H2O . H 4 HOH A 27 427 433 HOH H2O . H 4 HOH A 28 428 434 HOH H2O . H 4 HOH A 29 429 435 HOH H2O . H 4 HOH A 30 430 436 HOH H2O . H 4 HOH A 31 431 437 HOH H2O . H 4 HOH A 32 432 439 HOH H2O . H 4 HOH A 33 433 440 HOH H2O . H 4 HOH A 34 434 443 HOH H2O . H 4 HOH A 35 435 444 HOH H2O . H 4 HOH A 36 436 446 HOH H2O . H 4 HOH A 37 437 447 HOH H2O . H 4 HOH A 38 438 448 HOH H2O . H 4 HOH A 39 439 449 HOH H2O . H 4 HOH A 40 440 450 HOH H2O . H 4 HOH A 41 441 451 HOH H2O . H 4 HOH A 42 442 452 HOH H2O . H 4 HOH A 43 443 453 HOH H2O . H 4 HOH A 44 444 454 HOH H2O . H 4 HOH A 45 445 460 HOH H2O . H 4 HOH A 46 446 461 HOH H2O . H 4 HOH A 47 447 462 HOH H2O . H 4 HOH A 48 448 465 HOH H2O . H 4 HOH A 49 449 466 HOH H2O . H 4 HOH A 50 450 468 HOH H2O . H 4 HOH A 51 451 471 HOH H2O . H 4 HOH A 52 452 472 HOH H2O . H 4 HOH A 53 453 473 HOH H2O . H 4 HOH A 54 454 474 HOH H2O . H 4 HOH A 55 455 475 HOH H2O . H 4 HOH A 56 456 476 HOH H2O . H 4 HOH A 57 457 477 HOH H2O . H 4 HOH A 58 458 1 HOH H2O . H 4 HOH A 59 459 2 HOH H2O . I 4 HOH B 1 414 414 HOH H2O . I 4 HOH B 2 415 415 HOH H2O . I 4 HOH B 3 416 416 HOH H2O . I 4 HOH B 4 422 422 HOH H2O . I 4 HOH B 5 426 426 HOH H2O . I 4 HOH B 6 432 432 HOH H2O . I 4 HOH B 7 438 438 HOH H2O . I 4 HOH B 8 441 441 HOH H2O . I 4 HOH B 9 442 442 HOH H2O . I 4 HOH B 10 445 445 HOH H2O . I 4 HOH B 11 455 455 HOH H2O . I 4 HOH B 12 456 456 HOH H2O . I 4 HOH B 13 457 457 HOH H2O . I 4 HOH B 14 458 458 HOH H2O . I 4 HOH B 15 459 459 HOH H2O . I 4 HOH B 16 463 463 HOH H2O . I 4 HOH B 17 464 464 HOH H2O . I 4 HOH B 18 467 467 HOH H2O . I 4 HOH B 19 469 469 HOH H2O . I 4 HOH B 20 470 470 HOH H2O . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 N N1 UMP . . . G 3 -13.184 40.924 38.791 1 38.44 ? N1 UMP 337 B 1 HETATM 2 C C2 UMP . . . G 3 -12.745 39.771 38.091 1 41.7 ? C2 UMP 337 B 1 HETATM 3 N N3 UMP . . . G 3 -11.565 39.827 37.396 1 45.38 ? N3 UMP 337 B 1 HETATM 4 C C4 UMP . . . G 3 -10.697 40.926 37.29 1 39.64 ? C4 UMP 337 B 1 HETATM 5 C C5 UMP . . . G 3 -11.149 42.092 37.991 1 37.21 ? C5 UMP 337 B 1 HETATM 6 C C6 UMP . . . G 3 -12.332 41.992 38.668 1 35.5 ? C6 UMP 337 B 1 HETATM 7 O O2 UMP . . . G 3 -13.332 38.769 38.074 1 44.65 ? O2 UMP 337 B 1 HETATM 8 O O4 UMP . . . G 3 -9.671 40.915 36.666 1 45.73 ? O4 UMP 337 B 1 HETATM 9 C C1' UMP . . . G 3 -14.297 41.098 39.531 1 36.12 ? C1' UMP 337 B 1 HETATM 10 C C2' UMP . . . G 3 -14.266 41.135 41.128 1 26.17 ? C2' UMP 337 B 1 HETATM 11 C C3' UMP . . . G 3 -14.472 42.614 41.478 1 30.94 ? C3' UMP 337 B 1 HETATM 12 C C4' UMP . . . G 3 -15.418 43.101 40.346 1 37.64 ? C4' UMP 337 B 1 HETATM 13 O O3' UMP . . . G 3 -14.959 42.869 42.77 1 26.39 ? O3' UMP 337 B 1 HETATM 14 O O4' UMP . . . G 3 -15.07 42.309 39.167 1 37.76 ? O4' UMP 337 B 1 HETATM 15 C C5' UMP . . . G 3 -15.439 44.49 40.081 1 43.25 ? C5' UMP 337 B 1 HETATM 16 O O5' UMP . . . G 3 -14.427 44.966 39.33 1 49.37 ? O5' UMP 337 B 1 HETATM 17 P P UMP . . . G 3 -14.01 46.416 38.878 1 45.12 ? P UMP 337 B 1 HETATM 18 O OP1 UMP . . . G 3 -12.773 46.39 38.028 1 45.82 ? OP1 UMP 337 B 1 HETATM 19 O OP2 UMP . . . G 3 -13.812 47.092 40.364 1 44.6 ? OP2 UMP 337 B 1 HETATM 20 O OP3 UMP . . . G 3 -15.264 46.92 38.157 1 51.93 ? OP3 UMP 337 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 346 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 20 #